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APT reads compiler data via the model APIs. We've run into a race condition with these APIs as follows: 1) User has a third-party builder that runs before the JavaBuilder and creates a number of Java source files via the IResource APIs 2) APT runs and uses the model APIs to attempt to find some of those generated source files. This fails, as the model has not yet been refreshed. The JavaBuilder never encounters this problem directly, as it does not use the model for compilation during build.
The Java model can only be up-to-date iff a Java model API is used, or after a resource change event has been received. A workaround for APT would be to force the resource change event to be triggered using IWorkspace#checkpoint(boolean). No action planned on JDT/Core side.